Side-chain rotamer prediction is one of the most critical late stages in protein 3D structure building. Highly advanced and specialized algorithms (e.g., FASPR, RASP, SCWRL4, and SCWRL4v) optimize this process by use of rotamer libraries, combinatorial searches, and scoring functions. We seek to identify the sources of key rotamer errors as a basis for correcting and improving the accuracy of protein modeling going forward. In order to evaluate the aforementioned programs, we process 2496 high-quality single-chained all-atom filtered 30% homology protein 3D structures and use discretized rotamer analysis to compare original with calculated structures. Among 513,024 filtered residue records, increased amino acid residue-dependent rotamer errors─associated in particular with polar and charged amino acid residues (ARG, LYS, and GLN)─clearly correlate with increased amino acid residue solvent accessibility and an increased residue tendency toward the adoption of non-canonical off rotamers which modeling programs struggle to predict accurately. Understanding the impact of solvent accessibility now appears key to improved side-chain prediction accuracies.

Department of Chemistry and Biochemistry Mendel University in Brno Zemědělská 1665 1 CZ 613 00 Brno Czech Republic

KP Therapeutics s r o Purkyňova 649 127 CZ 612 00 Brno Czech Republic

Veterinary Research Institute Hudcova 296 70 CZ 621 00 Brno Czech Republic

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